2 papers
q-bio.GN2018
FPGA Acceleration of Short Read Alignment
Nathaniel McVicar, Akina Hoshino, Anna La Torre +3
Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and f…
q-bio.QM2012
Compression of next-generation sequencing reads aided by highly efficient de novo assembly
Daniel C. Jones, Walter L. Ruzzo, Xinxia Peng +1
We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we…